Casal2 Test Case MPD comparisons for SCI

1 SCI comparison of CASAL and Casal2 model configurations

This document compares the results of at least 2 CASAL model configurations (base and at least one sensitivity) and up to 6 Casal2 model configurations (3 BetaDiff and 3 ADOL-C).

The CASAL model sensitivity 1 has a smaller minimisation tolerance value than the CASAL base model (1e-8 vs. 2e-6).

The Casal2 ADOL-C and BetaDiff low tolerance models have the same tolerance values than the CASAL base model (1e-8 vs. 2e-6).

1.1 SCI model characteristics

The main characteristics of the Test Case SCI (Scampi) CASAL model are:

• length-based sex-specific model
• years 1986 - 2022, projection years 2023 - 2027
• three time steps, Oct - Jan, Feb - Apr, May - Sep
• estimate growth transition matrix
• dour tag releases
• Beverton-Holt stock-recruitment relationship, with steepness (h) 0.75 and \(CV_R\) 0.7 (prior)
• length-weight relationship (\(W = aL^b\))
• three fisheries

Observation data include:

• trawl fishery CPUE
• trawl survey abundance and proportions-at-length
• fishery proportions-at-length
• tag-recapture data for growth estimation
• maturity data

Parameters estimated include:

• B0
• sex-specific growth parameters
• maturity parameters
• YCS (recruitment deviations)
• sex-specific fishery and trawl selectivity parameters

1.2 R environment

## [1] "Wed Aug 17 16:41:45 2022"
## R version 3.6.0 (2019-04-26)
## Platform: x86_64-redhat-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
## 
## Matrix products: default
## BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_GB.UTF_8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] Casal2_22.08   casal_2.30     devtools_2.4.4 usethis_2.1.6  rlist_0.4.6.2 
##  [6] ggthemes_4.2.4 gridExtra_2.3  coda_0.19-4    ggmcmc_1.5.1.1 ggplot2_3.3.6 
## [11] tidyr_1.2.0    huxtable_5.5.0 dplyr_1.0.9    plyr_1.8.7    
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.9         lattice_0.20-38    prettyunits_1.1.1  ps_1.7.1          
##  [5] assertthat_0.2.1   digest_0.6.29      utf8_1.2.2         mime_0.12         
##  [9] R6_2.5.1           evaluate_0.16      pillar_1.8.0       rlang_1.0.4       
## [13] rstudioapi_0.13    data.table_1.14.2  miniUI_0.1.1.1     urlchecker_1.0.1  
## [17] callr_3.7.1        jquerylib_0.1.4    rmarkdown_2.15     stringr_1.4.0     
## [21] htmlwidgets_1.5.4  munsell_0.5.0      shiny_1.7.2        compiler_3.6.0    
## [25] httpuv_1.6.5       xfun_0.32          pkgconfig_2.0.3    pkgbuild_1.3.1    
## [29] htmltools_0.5.3    tidyselect_1.1.2   tibble_3.1.8       reshape_0.8.9     
## [33] fansi_1.0.3        crayon_1.5.1       withr_2.5.0        later_1.3.0       
## [37] grid_3.6.0         jsonlite_1.8.0     xtable_1.8-4       GGally_2.1.2      
## [41] gtable_0.3.0       lifecycle_1.0.1    DBI_1.1.3          magrittr_2.0.3    
## [45] scales_1.2.0       cli_3.3.0          stringi_1.7.8      cachem_1.0.6      
## [49] remotes_2.4.2      fs_1.5.2           promises_1.2.0.1   bslib_0.4.0       
## [53] ellipsis_0.3.2     generics_0.1.3     vctrs_0.4.1        RColorBrewer_1.1-3
## [57] tools_3.6.0        glue_1.6.2         purrr_0.3.4        pkgload_1.3.0     
## [61] processx_3.7.0     fastmap_1.1.0      yaml_2.3.5         colorspace_2.0-3  
## [65] sessioninfo_1.2.2  memoise_2.0.1      knitr_1.39         profvis_0.3.7     
## [69] sass_0.4.2

1.3 CASAL and Casal2 model output

source('../../R-functions/report_read_in_CASAL_MPD_files.R')

source('../../R-functions/report_read_in_Casal2_MPD_files.R')

1.4 Tables

Tables of parameter estimates and objective function components for the CASAL and Casal2 model MPD results

CASAL parameter estimates

rownames	Base_Model	Sensitivity_1	Percent_Diff
initialization.B0	2106.00000	2106.00000	0.000
growth[1].minsigma_male	4.51900	4.51900	0.000
recruitment.YCS1	0.26100	0.26100	0.000
recruitment.YCS2	0.28190	0.28190	0.000
recruitment.YCS3	0.35370	0.35370	0.000
recruitment.YCS4	0.54940	0.54940	0.000
recruitment.YCS5	3.08000	3.08000	0.000
recruitment.YCS6	0.61570	0.61570	0.000
recruitment.YCS7	0.60020	0.60020	0.000
recruitment.YCS8	0.50630	0.50630	0.000
recruitment.YCS9	0.31460	0.31460	0.000
recruitment.YCS10	0.38550	0.38550	0.000
recruitment.YCS11	0.39680	0.39680	0.000
recruitment.YCS12	0.37270	0.37270	0.000
recruitment.YCS13	0.49890	0.49890	0.000
recruitment.YCS14	0.37530	0.37530	0.000
recruitment.YCS15	0.49940	0.49940	0.000
recruitment.YCS16	0.53520	0.53520	0.000
recruitment.YCS17	0.59340	0.59340	0.000
recruitment.YCS18	0.36560	0.36560	0.000
recruitment.YCS19	0.59920	0.59920	0.000
recruitment.YCS20	0.46420	0.46420	0.000
recruitment.YCS21	0.49390	0.49390	0.000
recruitment.YCS22	0.55130	0.55130	0.000
recruitment.YCS23	0.98750	0.98750	0.000
recruitment.YCS24	0.53080	0.53080	0.000
recruitment.YCS25	0.88540	0.88540	0.000
recruitment.YCS26	0.91310	0.91310	0.000
recruitment.YCS27	0.51160	0.51160	0.000
recruitment.YCS28	0.64290	0.64290	0.000
recruitment.YCS29	0.44980	0.44990	-0.022
recruitment.YCS30	0.62760	0.62760	0.000
recruitment.YCS31	0.58150	0.58150	0.000
recruitment.YCS32	0.55560	0.55550	0.018
recruitment.YCS33	0.93870	0.93870	0.000
recruitment.YCS34	1.41700	1.41700	0.000
recruitment.YCS35	0.39340	0.39340	0.000
recruitment.YCS36	0.47900	0.47900	0.000
recruitment.YCS37	0.54990	0.54980	0.018
maturity_props.all1	30.12000	30.12000	0.000
maturity_props.all2	7.09300	7.09300	0.000
selectivity[FishingSel_1].female1	43.92000	43.92000	0.000
selectivity[FishingSel_1].female2	16.37000	16.37000	0.000
selectivity[FishingSel_1].female3	0.85520	0.85520	0.000
selectivity[FishingSel_1].female4	1.00000	1.00000	0.000
selectivity[FishingSel_2].female1	45.43000	45.43000	0.000
selectivity[FishingSel_2].female2	20.02000	20.02000	0.000
selectivity[FishingSel_2].female3	0.50660	0.50660	0.000
selectivity[FishingSel_2].female4	1.00000	1.00000	0.000
selectivity[TrawlSurveySel_1].female1	30.69000	30.69000	0.000
selectivity[TrawlSurveySel_1].female2	20.77000	20.77000	0.000
selectivity[TrawlSurveySel_1].female3	1.12900	1.12900	0.000
selectivity[TrawlSurveySel_1].female4	1.00000	1.00000	0.000
selectivity[TrawlSurveySel_2].female1	36.98000	36.98000	0.000
selectivity[TrawlSurveySel_2].female2	16.94000	16.94000	0.000
selectivity[TrawlSurveySel_2].female3	1.08700	1.08700	0.000
selectivity[TrawlSurveySel_2].female4	1.00000	1.00000	0.000
growth[1].g_male1	13.86000	13.86000	0.000
growth[1].g_male2	2.84700	2.84700	0.000
growth[1].g_female1	13.42000	13.42000	0.000
growth[1].g_female2	0.92490	0.92490	0.000

Casal2 parameter estimates

rownames	betadiff_casal_flags_on	betadiff_casal_flags_off	betadiff_casal_flags_on_low_tol
process[Recruitment].b0	2105.51000	2107.57000	2105.51000
growth_increment[female_growth].min_sigma	4.51884	4.59666	4.51885
process[Recruitment].ycs_values{1985}	0.26103	0.26061	0.26104
process[Recruitment].ycs_values{1986}	0.28188	0.28134	0.28188
process[Recruitment].ycs_values{1987}	0.35365	0.35004	0.35365
process[Recruitment].ycs_values{1988}	0.54947	0.52944	0.54944
process[Recruitment].ycs_values{1989}	3.07992	3.14872	3.07993
process[Recruitment].ycs_values{1990}	0.61596	0.60963	0.61598
process[Recruitment].ycs_values{1991}	0.60021	0.59400	0.60020
process[Recruitment].ycs_values{1992}	0.50628	0.50365	0.50628
process[Recruitment].ycs_values{1993}	0.31465	0.31539	0.31465
process[Recruitment].ycs_values{1994}	0.38549	0.38173	0.38549
process[Recruitment].ycs_values{1995}	0.39678	0.39896	0.39678
process[Recruitment].ycs_values{1996}	0.37269	0.37413	0.37269
process[Recruitment].ycs_values{1997}	0.49890	0.49986	0.49890
process[Recruitment].ycs_values{1998}	0.37530	0.37426	0.37530
process[Recruitment].ycs_values{1999}	0.49939	0.50199	0.49939
process[Recruitment].ycs_values{2000}	0.53521	0.53824	0.53521
process[Recruitment].ycs_values{2001}	0.59334	0.59800	0.59334
process[Recruitment].ycs_values{2002}	0.36562	0.36432	0.36562
process[Recruitment].ycs_values{2003}	0.59914	0.60293	0.59914
process[Recruitment].ycs_values{2004}	0.46422	0.46358	0.46423
process[Recruitment].ycs_values{2005}	0.49389	0.49422	0.49389
process[Recruitment].ycs_values{2006}	0.55124	0.55346	0.55125
process[Recruitment].ycs_values{2007}	0.98745	0.99690	0.98745
process[Recruitment].ycs_values{2008}	0.53079	0.53290	0.53080
process[Recruitment].ycs_values{2009}	0.88537	0.88413	0.88537
process[Recruitment].ycs_values{2010}	0.91311	0.92624	0.91312
process[Recruitment].ycs_values{2011}	0.51160	0.50437	0.51161
process[Recruitment].ycs_values{2012}	0.64287	0.64713	0.64286
process[Recruitment].ycs_values{2013}	0.44984	0.45272	0.44985
process[Recruitment].ycs_values{2014}	0.62763	0.62466	0.62761
process[Recruitment].ycs_values{2015}	0.58153	0.58255	0.58154
process[Recruitment].ycs_values{2016}	0.55554	0.55794	0.55554
process[Recruitment].ycs_values{2017}	0.93876	0.94112	0.93875
process[Recruitment].ycs_values{2018}	1.41706	1.43303	1.41707
process[Recruitment].ycs_values{2019}	0.39340	0.38899	0.39339
process[Recruitment].ycs_values{2020}	0.47898	0.47810	0.47900
process[Recruitment].ycs_values{2021}	0.54989	0.54986	0.54982
selectivity[maturity].a50	30.11660	30.11660	30.11660
selectivity[maturity].ato95	7.09305	7.09305	7.09305
selectivity[FishingSel_1_male].a50	43.92180	44.21950	43.92180
selectivity[FishingSel_1_male].ato95	16.36960	16.52750	16.36950
selectivity[FishingSel_1_male].alpha	0.85518	0.85424	0.85518
selectivity[FishingSel_2_female].a50	45.42970	45.77970	45.42960
selectivity[FishingSel_2_female].ato95	20.02320	20.18150	20.02320
selectivity[FishingSel_2_male].alpha	0.50661	0.50648	0.50662
selectivity[TrawlSurveySel_1_female].a50	30.69370	31.00400	30.69360
selectivity[TrawlSurveySel_1_female].ato95	20.77060	21.74160	20.77030
selectivity[TrawlSurveySel_1_male].alpha	1.12877	1.12748	1.12876
selectivity[TrawlSurveySel_2_female].a50	36.98430	37.22380	36.98430
selectivity[TrawlSurveySel_2_female].ato95	16.94280	17.18710	16.94280
selectivity[TrawlSurveySel_2_male].alpha	1.08687	1.08665	1.08687
growth_increment[male_growth].g_alpha	13.85690	13.83850	13.85690
growth_increment[male_growth].g_beta	2.84680	2.74853	2.84680
growth_increment[female_growth].g_alpha	13.42240	13.42640	13.42240
growth_increment[female_growth].g_beta	0.92508	0.80358	0.92508

Casal2 parameter estimates: Percent Difference from betadiff_casal_flags_on

rownames	betadiff_casal_flags_on	betadiff_casal_flags_off	betadiff_casal_flags_on_low_tol
process[Recruitment].b0	0.000	-0.098	0.000
growth_increment[female_growth].min_sigma	0.000	-1.722	-0.000
process[Recruitment].ycs_values{1985}	0.000	0.161	-0.003
process[Recruitment].ycs_values{1986}	0.000	0.191	-0.001
process[Recruitment].ycs_values{1987}	0.000	1.023	0.001
process[Recruitment].ycs_values{1988}	0.000	3.646	0.005
process[Recruitment].ycs_values{1989}	0.000	-2.234	-0.000
process[Recruitment].ycs_values{1990}	0.000	1.028	-0.003
process[Recruitment].ycs_values{1991}	0.000	1.033	0.001
process[Recruitment].ycs_values{1992}	0.000	0.518	-0.000
process[Recruitment].ycs_values{1993}	0.000	-0.238	-0.001
process[Recruitment].ycs_values{1994}	0.000	0.976	0.001
process[Recruitment].ycs_values{1995}	0.000	-0.550	-0.002
process[Recruitment].ycs_values{1996}	0.000	-0.386	0.001
process[Recruitment].ycs_values{1997}	0.000	-0.192	-0.000
process[Recruitment].ycs_values{1998}	0.000	0.277	-0.001
process[Recruitment].ycs_values{1999}	0.000	-0.521	-0.001
process[Recruitment].ycs_values{2000}	0.000	-0.567	0.000
process[Recruitment].ycs_values{2001}	0.000	-0.786	-0.000
process[Recruitment].ycs_values{2002}	0.000	0.356	-0.001
process[Recruitment].ycs_values{2003}	0.000	-0.631	0.001
process[Recruitment].ycs_values{2004}	0.000	0.140	-0.001
process[Recruitment].ycs_values{2005}	0.000	-0.066	0.000
process[Recruitment].ycs_values{2006}	0.000	-0.401	-0.000
process[Recruitment].ycs_values{2007}	0.000	-0.957	0.001
process[Recruitment].ycs_values{2008}	0.000	-0.398	-0.002
process[Recruitment].ycs_values{2009}	0.000	0.140	0.000
process[Recruitment].ycs_values{2010}	0.000	-1.437	-0.000
process[Recruitment].ycs_values{2011}	0.000	1.414	-0.001
process[Recruitment].ycs_values{2012}	0.000	-0.663	0.002
process[Recruitment].ycs_values{2013}	0.000	-0.640	-0.004
process[Recruitment].ycs_values{2014}	0.000	0.473	0.002
process[Recruitment].ycs_values{2015}	0.000	-0.175	-0.001
process[Recruitment].ycs_values{2016}	0.000	-0.431	0.000
process[Recruitment].ycs_values{2017}	0.000	-0.252	0.000
process[Recruitment].ycs_values{2018}	0.000	-1.127	-0.001
process[Recruitment].ycs_values{2019}	0.000	1.121	0.003
process[Recruitment].ycs_values{2020}	0.000	0.183	-0.004
process[Recruitment].ycs_values{2021}	0.000	0.005	0.012
selectivity[maturity].a50	0.000	0.000	0.000
selectivity[maturity].ato95	0.000	0.000	0.000
selectivity[FishingSel_1_male].a50	0.000	-0.678	0.000
selectivity[FishingSel_1_male].ato95	0.000	-0.965	0.001
selectivity[FishingSel_1_male].alpha	0.000	0.110	0.000
selectivity[FishingSel_2_female].a50	0.000	-0.770	0.000
selectivity[FishingSel_2_female].ato95	0.000	-0.791	0.000
selectivity[FishingSel_2_male].alpha	0.000	0.027	-0.000
selectivity[TrawlSurveySel_1_female].a50	0.000	-1.011	0.000
selectivity[TrawlSurveySel_1_female].ato95	0.000	-4.675	0.001
selectivity[TrawlSurveySel_1_male].alpha	0.000	0.114	0.001
selectivity[TrawlSurveySel_2_female].a50	0.000	-0.648	0.000
selectivity[TrawlSurveySel_2_female].ato95	0.000	-1.442	0.000
selectivity[TrawlSurveySel_2_male].alpha	0.000	0.020	0.000
growth_increment[male_growth].g_alpha	0.000	0.133	0.000
growth_increment[male_growth].g_beta	0.000	3.452	0.000
growth_increment[female_growth].g_alpha	0.000	-0.030	0.000
growth_increment[female_growth].g_beta	0.000	13.134	-0.000

CASAL objective function component values

Component	Base_Model	Sensitivity_1
CPUE-Trawl_1	17.230	17.230
TrawlSurvey_1	-5.390	-5.390
TrawlSurvey_2	15.850	15.850
TrawlSurveyProportionAtLength_1	675.000	675.000
TrawlSurveyProportionAtLength_2	878.300	878.300
CommercialCatchLength_1	2022.000	2022.000
CommercialCatchLength_2	1470.000	1470.000
CommercialCatchLength_3	1434.000	1434.000
Cryer_Oliver_maturity	84.060	84.060
1997-recaptures1-1	31.160	31.160
1997-recaptures1-2	61.740	61.740
1997-recaptures2-1	15.140	15.140
1997-recaptures2-2	34.650	34.650
1997-recaptures2-3	27.940	27.940
1997-recaptures3-1	22.850	22.850
1997-recaptures3-2	65.330	65.330
1997-recaptures3-3	58.950	58.950
prior_on_initialization.B0	7.652	7.652
prior_on_growth[1].minsigma_male	0.000	0.000
prior_on_recruitment.YCS	-5.344	-5.344
prior_on_maturity_props.all	0.000	0.000
prior_on_selectivity[FishingSel_1].female	0.000	0.000
prior_on_selectivity[FishingSel_2].female	0.000	0.000
prior_on_selectivity[TrawlSurveySel_1].female	0.000	0.000
prior_on_selectivity[TrawlSurveySel_2].female	0.000	0.000
prior_on_growth[1].g_male	0.000	0.000
prior_on_growth[1].g_female	0.000	0.000
prior_on_q_CPUE-Commercialq_1	-6.457	-6.457
prior_on_q_TrawlSurveyq_1	-2.477	-2.477
prior_on_q_TrawlSurveyq_2	-2.349	-2.349
Penalty_Trawl_1_Catch	0.000	0.000
Penalty_Trawl_2_Catch	0.000	0.000
Penalty_Trawl_3_Catch	0.000	0.000
Total	6899.000	6899.000

Casal2 objective function component values

rownames	betadiff_casal_flags_on	betadiff_casal_flags_off	betadiff_casal_flags_on_low_tol
observation->CPUE-Trawl_1->1990	-2.370	-2.374	-2.370
observation->CPUE-Trawl_1->1991	5.552	5.528	5.552
observation->CPUE-Trawl_1->1992	-0.556	-0.527	-0.556
observation->CPUE-Trawl_1->1993	8.941	8.869	8.941
observation->CPUE-Trawl_1->1994	-0.466	-0.440	-0.466
observation->CPUE-Trawl_1->1995	5.854	5.819	5.854
observation->CPUE-Trawl_1->1996	-2.204	-2.208	-2.204
observation->CPUE-Trawl_1->1997	2.870	2.865	2.870
observation->CPUE-Trawl_1->1998	-2.241	-2.238	-2.241
observation->CPUE-Trawl_1->1999	7.105	7.082	7.105
observation->CPUE-Trawl_1->2000	-1.373	-1.390	-1.373
observation->CPUE-Trawl_1->2001	-0.310	-0.273	-0.310
observation->CPUE-Trawl_1->2002	-0.305	-0.342	-0.305
observation->CPUE-Trawl_1->2003	-2.020	-2.028	-2.020
observation->CPUE-Trawl_1->2004	1.495	1.490	1.495
observation->CPUE-Trawl_1->2005	-0.394	-0.396	-0.394
observation->CPUE-Trawl_1->2006	-2.180	-2.182	-2.180
observation->CPUE-Trawl_1->2007	-1.392	-1.394	-1.392
observation->CPUE-Trawl_1->2008	-1.224	-1.231	-1.224
observation->CPUE-Trawl_1->2009	-2.417	-2.417	-2.417
observation->CPUE-Trawl_1->2010	-0.496	-0.509	-0.496
observation->CPUE-Trawl_1->2011	1.668	1.641	1.668
observation->CPUE-Trawl_1->2012	4.982	4.943	4.982
observation->CPUE-Trawl_1->2013	2.770	2.803	2.770
observation->CPUE-Trawl_1->2014	-0.613	-0.606	-0.613
observation->CPUE-Trawl_1->2015	1.211	1.206	1.211
observation->CPUE-Trawl_1->2016	2.468	2.478	2.468
observation->CPUE-Trawl_1->2017	-0.629	-0.633	-0.629
observation->CPUE-Trawl_1->2018	-2.289	-2.294	-2.289
observation->CPUE-Trawl_1->2019	-0.259	-0.239	-0.259
observation->CPUE-Trawl_1->2020	-1.731	-1.729	-1.731
observation->CPUE-Trawl_1->2021	-2.221	-2.221	-2.221
observation->TrawlSurvey_1->1993	-1.801	-1.799	-1.801
observation->TrawlSurvey_1->1994	-1.820	-1.820	-1.820
observation->TrawlSurvey_1->1995	-1.721	-1.721	-1.721
observation->TrawlSurvey_1->2004	-0.048	-0.038	-0.048
observation->TrawlSurvey_2->2003	-0.491	-0.490	-0.491
observation->TrawlSurvey_2->2005	-0.901	-0.901	-0.901
observation->TrawlSurvey_2->2006	-0.988	-0.988	-0.988
observation->TrawlSurvey_2->2012	8.206	8.197	8.206
observation->TrawlSurvey_2->2015	-1.238	-1.238	-1.238
observation->TrawlSurvey_2->2018	12.343	12.321	12.343
observation->TrawlSurvey_2->2021	-1.079	-1.079	-1.079
observation->TrawlSurveyProportionAtLength_1->1993	140.116	140.149	140.117
observation->TrawlSurveyProportionAtLength_1->1994	136.075	136.211	136.075
observation->TrawlSurveyProportionAtLength_1->1995	134.809	134.741	134.809
observation->TrawlSurveyProportionAtLength_1->2004	136.719	136.752	136.719
observation->TrawlSurveyProportionAtLength_1->2021	127.242	127.234	127.242
observation->TrawlSurveyProportionAtLength_2->2003	122.195	122.196	122.195
observation->TrawlSurveyProportionAtLength_2->2005	127.870	127.854	127.870
observation->TrawlSurveyProportionAtLength_2->2006	132.110	131.974	132.110
observation->TrawlSurveyProportionAtLength_2->2012	131.462	131.375	131.462
observation->TrawlSurveyProportionAtLength_2->2015	119.936	119.991	119.936
observation->TrawlSurveyProportionAtLength_2->2018	125.164	125.341	125.164
observation->TrawlSurveyProportionAtLength_2->2021	119.526	119.560	119.526
observation->CommercialCatchLength_1->1992	68.899	68.873	68.899
observation->CommercialCatchLength_1->1993	85.879	85.725	85.879
observation->CommercialCatchLength_1->1996	147.667	147.860	147.667
observation->CommercialCatchLength_1->1997	84.247	84.124	84.247
observation->CommercialCatchLength_1->1998	117.490	117.428	117.490
observation->CommercialCatchLength_1->1999	139.920	139.921	139.920
observation->CommercialCatchLength_1->2000	115.382	115.345	115.382
observation->CommercialCatchLength_1->2001	123.573	123.520	123.573
observation->CommercialCatchLength_1->2002	94.877	94.777	94.877
observation->CommercialCatchLength_1->2003	152.191	151.986	152.191
observation->CommercialCatchLength_1->2005	93.313	93.192	93.313
observation->CommercialCatchLength_1->2008	154.113	154.375	154.113
observation->CommercialCatchLength_1->2011	112.774	112.747	112.774
observation->CommercialCatchLength_1->2012	153.745	153.501	153.745
observation->CommercialCatchLength_1->2013	109.472	109.380	109.472
observation->CommercialCatchLength_1->2014	93.145	93.155	93.145
observation->CommercialCatchLength_1->2020	174.821	174.725	174.821
observation->CommercialCatchLength_2->1994	101.844	101.868	101.844
observation->CommercialCatchLength_2->1995	109.767	109.724	109.767
observation->CommercialCatchLength_2->1997	116.900	116.834	116.900
observation->CommercialCatchLength_2->1998	155.404	156.498	155.403
observation->CommercialCatchLength_2->1999	124.131	124.045	124.131
observation->CommercialCatchLength_2->2007	131.024	130.931	131.024
observation->CommercialCatchLength_2->2008	158.478	158.829	158.478
observation->CommercialCatchLength_2->2009	177.935	177.854	177.935
observation->CommercialCatchLength_2->2012	138.105	138.672	138.105
observation->CommercialCatchLength_2->2019	141.424	141.526	141.424
observation->CommercialCatchLength_2->2021	114.547	114.412	114.547
observation->CommercialCatchLength_3->1991	137.377	137.256	137.377
observation->CommercialCatchLength_3->1993	90.372	90.404	90.372
observation->CommercialCatchLength_3->1994	122.548	122.354	122.548
observation->CommercialCatchLength_3->1995	104.971	105.142	104.971
observation->CommercialCatchLength_3->1996	82.543	82.374	82.543
observation->CommercialCatchLength_3->1997	107.868	107.733	107.868
observation->CommercialCatchLength_3->2000	116.229	116.227	116.229
observation->CommercialCatchLength_3->2001	179.354	178.915	179.354
observation->CommercialCatchLength_3->2007	129.099	128.996	129.099
observation->CommercialCatchLength_3->2008	111.241	111.297	111.241
observation->CommercialCatchLength_3->2010	138.651	138.500	138.651
observation->CommercialCatchLength_3->2011	113.720	113.605	113.720
observation->Cryer_Oliver_maturity	84.057	84.057	84.057
observation->1997_recaptures1_1	31.165	31.189	31.165
observation->1997_recaptures1_2	61.740	61.740	61.740
observation->1997_recaptures2_1	15.136	15.133	15.136
observation->1997_recaptures2_2	34.649	34.639	34.649
observation->1997_recaptures2_3	27.938	27.938	27.938
observation->1997_recaptures3_1	22.851	22.821	22.851
observation->1997_recaptures3_2	65.328	65.499	65.328
observation->1997_recaptures3_3	58.948	58.946	58.948
prior->B0->process[Recruitment].b0	7.652	7.653	7.652
prior->growth_min_sigma->growth_increment[female_growth].min_sigma	0.000	0.000	0.000
prior->YCS->process[Recruitment].ycs_values{1985}	0.297	0.300	0.297
prior->YCS->process[Recruitment].ycs_values{1986}	0.161	0.164	0.161
prior->YCS->process[Recruitment].ycs_values{1987}	-0.155	-0.143	-0.155
prior->YCS->process[Recruitment].ycs_values{1988}	-0.399	-0.397	-0.399
prior->YCS->process[Recruitment].ycs_values{1989}	3.324	3.420	3.324
prior->YCS->process[Recruitment].ycs_values{1990}	-0.383	-0.385	-0.383
prior->YCS->process[Recruitment].ycs_values{1991}	-0.389	-0.391	-0.389
prior->YCS->process[Recruitment].ycs_values{1992}	-0.390	-0.389	-0.390
prior->YCS->process[Recruitment].ycs_values{1993}	-0.008	-0.011	-0.008
prior->YCS->process[Recruitment].ycs_values{1994}	-0.241	-0.232	-0.241
prior->YCS->process[Recruitment].ycs_values{1995}	-0.265	-0.270	-0.265
prior->YCS->process[Recruitment].ycs_values{1996}	-0.209	-0.213	-0.209
prior->YCS->process[Recruitment].ycs_values{1997}	-0.387	-0.387	-0.387
prior->YCS->process[Recruitment].ycs_values{1998}	-0.216	-0.213	-0.216
prior->YCS->process[Recruitment].ycs_values{1999}	-0.387	-0.388	-0.387
prior->YCS->process[Recruitment].ycs_values{2000}	-0.398	-0.398	-0.398
prior->YCS->process[Recruitment].ycs_values{2001}	-0.392	-0.390	-0.392
prior->YCS->process[Recruitment].ycs_values{2002}	-0.190	-0.186	-0.190
prior->YCS->process[Recruitment].ycs_values{2003}	-0.390	-0.388	-0.390
prior->YCS->process[Recruitment].ycs_values{2004}	-0.363	-0.362	-0.363
prior->YCS->process[Recruitment].ycs_values{2005}	-0.384	-0.385	-0.384
prior->YCS->process[Recruitment].ycs_values{2006}	-0.399	-0.399	-0.399
prior->YCS->process[Recruitment].ycs_values{2007}	0.031	0.045	0.031
prior->YCS->process[Recruitment].ycs_values{2008}	-0.397	-0.398	-0.397
prior->YCS->process[Recruitment].ycs_values{2009}	-0.114	-0.116	-0.114
prior->YCS->process[Recruitment].ycs_values{2010}	-0.076	-0.058	-0.076
prior->YCS->process[Recruitment].ycs_values{2011}	-0.392	-0.389	-0.392
prior->YCS->process[Recruitment].ycs_values{2012}	-0.368	-0.365	-0.368
prior->YCS->process[Recruitment].ycs_values{2013}	-0.348	-0.351	-0.348
prior->YCS->process[Recruitment].ycs_values{2014}	-0.377	-0.378	-0.377
prior->YCS->process[Recruitment].ycs_values{2015}	-0.395	-0.395	-0.395
prior->YCS->process[Recruitment].ycs_values{2016}	-0.399	-0.399	-0.399
prior->YCS->process[Recruitment].ycs_values{2017}	-0.040	-0.037	-0.040
prior->YCS->process[Recruitment].ycs_values{2018}	0.725	0.752	0.725
prior->YCS->process[Recruitment].ycs_values{2019}	-0.258	-0.249	-0.258
prior->YCS->process[Recruitment].ycs_values{2020}	-0.375	-0.374	-0.375
prior->YCS->process[Recruitment].ycs_values{2021}	-0.399	-0.399	-0.399
prior->maturity_a50->selectivity[maturity].a50	0.000	0.000	0.000
prior->maturity_ato95->selectivity[maturity].ato95	0.000	0.000	0.000
prior->FishingSel_1_a50->selectivity[FishingSel_1_male].a50	0.000	0.000	0.000
prior->FishingSel_1_ato95->selectivity[FishingSel_1_male].ato95	0.000	0.000	0.000
prior->FishingSel_1_male_alpha->selectivity[FishingSel_1_male].alpha	0.000	0.000	0.000
prior->FishingSel_2_a50->selectivity[FishingSel_2_female].a50	0.000	0.000	0.000
prior->FishingSel_2_ato95->selectivity[FishingSel_2_female].ato95	0.000	0.000	0.000
prior->FishingSel_2_male_alpha->selectivity[FishingSel_2_male].alpha	0.000	0.000	0.000
prior->TrawlSurveySel_1_a50->selectivity[TrawlSurveySel_1_female].a50	0.000	0.000	0.000
prior->TrawlSurveySel_1_ato95->selectivity[TrawlSurveySel_1_female].ato95	0.000	0.000	0.000
prior->TrawlSurveySel_1_male_alpha->selectivity[TrawlSurveySel_1_male].alpha	0.000	0.000	0.000
prior->TrawlSurveySel_2_a50->selectivity[TrawlSurveySel_2_female].a50	0.000	0.000	0.000
prior->TrawlSurveySel_2_ato95->selectivity[TrawlSurveySel_2_female].ato95	0.000	0.000	0.000
prior->TrawlSurveySel_2_male_alpha->selectivity[TrawlSurveySel_2_male].alpha	0.000	0.000	0.000
prior->g_alpha_male->growth_increment[male_growth].g_alpha	0.000	0.000	0.000
prior->g_beta_male->growth_increment[male_growth].g_beta	0.000	0.000	0.000
prior->g_alpha_female->growth_increment[female_growth].g_alpha	0.000	0.000	0.000
prior->g_beta_female->growth_increment[female_growth].g_beta	0.000	0.000	0.000
additional_prior->CPUE-Commercialq_1	-6.457	-6.436	-6.457
additional_prior->TrawlSurveyq_1	-2.477	-2.460	-2.477
additional_prior->TrawlSurveyq_2	-2.349	-2.336	-2.349
total_score	6898.790	6898.740	6898.790

## [1] "CASAL base model convergence information"
## [1] "Minimiser convergence threshold: 2e-06"                                                                   
## [2] "Minimiser achieved convergence after 119 quasi-Newton iterations using 126 objective function evaluations"
## [1] ""
## [1] "CASAL sensitivity 1 model convergence information"
## [1] "Minimiser convergence threshold: 1e-08"                                                                   
## [2] "Minimiser achieved convergence after 134 quasi-Newton iterations using 153 objective function evaluations"
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model convergence information"
## [1] "fmm: have converged: t = 1.64873e-06 f = 6898.79"
## [2] "Successful convergence in optimise"              
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model convergence information"
## [1] "fmm: have converged: t = 1.83524e-06 f = 6898.74"
## [2] "Successful convergence in optimise"              
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model convergence information"
## [1] "fmm: have converged: t = 2.30345e-09 f = 6898.79"
## [2] "Successful convergence in optimise"

## [1] "CASAL model warnings"
## NULL
## [1] ""
## [1] "CASAL sensitivity 1 model warnings"
## NULL
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model warnings"
## [1] ""
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model warnings"
## [1] ""
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model warnings"
## [1] ""

1.5 Matching of outputs

Time series comparisons with CASAL base model results

## [1] "Catch time series base model comparison for run betadiff_casal_flags_on"
## [1] "Actual catches for Trawl 1 match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_off"
## [1] "Actual catches for Trawl 1 match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_on_low_tol"
## [1] "Actual catches for Trawl 1 match: yes"
## [1] ""

## [1] "Catch time series base model comparison for run betadiff_casal_flags_on"
## [1] "Actual catches for Trawl 2 match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_off"
## [1] "Actual catches for Trawl 2 match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_on_low_tol"
## [1] "Actual catches for Trawl 2 match: yes"
## [1] ""

## [1] "Catch time series base model comparison for run betadiff_casal_flags_on"
## [1] "Actual catches for Trawl 3 match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_off"
## [1] "Actual catches for Trawl 3 match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_on_low_tol"
## [1] "Actual catches for Trawl 3 match: yes"
## [1] ""

Derived quantities

SB0, SBcurrent, MSY, F_MSY, others…

1.6 Plots

Comparison plots

## [1] "CASAL base parameter correlation range (excluding 1.0): -0.9193 0.9407"

## [1] "CASAL sensitivity 1 parameter correlation range (excluding 1.0): -0.9193 0.94"

## [1] "Casal2 betadiff_casal_flags_on parameter correlation range (excluding 1.0): -0.919151 0.940771"

## [1] "Casal2 betadiff_casal_flags_off parameter correlation range (excluding 1.0): -0.922937 0.943642"

## [1] "Casal2 betadiff_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.920111 0.939971"